debian/changelog

+bedops (2.4.36+dfsg-2) UNRELEASED; urgency=medium
+  
+  * Team upload.
+  * Use 2to3 to port python files from python2 to python3
+    Closes: #936197
+
+ -- Shayan Doust <hello@shayandoust.me>  Fri, 13 Sep 2019 15:10:57 +0100
+
 bedops (2.4.36+dfsg-1) unstable; urgency=medium
 
   * Team upload.

debian/patches/2to3.patch

+Description: port python files using python2 to python3
+Author: Shayan Doust <hello@shayandoust.me>
+Bug-Debian: https://bugs.debian.org/936197
+Last-Update: 2019-09-13
+---
+
+Index: bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
+===================================================================
+--- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py	2019-09-13 15:06:08.879696791 +0100
++++ bedops/applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py	2019-09-13 15:06:08.871696823 +0100
+@@ -19,7 +19,7 @@
+ #    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ #
+ 
+-from __future__ import absolute_import, division, print_function, unicode_literals
++
+ 
+ import sys
+ import os
+Index: bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py
+===================================================================
+--- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-slurm.py	2019-09-13 15:06:08.879696791 +0100
++++ bedops/applications/bed/sort-bed/src/update-sort-bed-slurm.py	2019-09-13 15:06:08.871696823 +0100
+@@ -19,7 +19,7 @@
+ #    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ #
+ 
+-from __future__ import absolute_import, division, print_function, unicode_literals
++
+ 
+ import sys
+ import os
+Index: bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
+===================================================================
+--- bedops.orig/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py	2019-09-13 15:06:08.879696791 +0100
++++ bedops/applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py	2019-09-13 15:06:08.871696823 +0100
+@@ -19,7 +19,7 @@
+ #    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ #
+ 
+-from __future__ import absolute_import, division, print_function, unicode_literals
++
+ 
+ import sys
+ import os
+Index: bedops/applications/bed/starch/src/starch-diff.py
+===================================================================
+--- bedops.orig/applications/bed/starch/src/starch-diff.py	2019-09-13 15:06:08.879696791 +0100
++++ bedops/applications/bed/starch/src/starch-diff.py	2019-09-13 15:06:08.871696823 +0100
+@@ -19,7 +19,7 @@
+ #    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ #
+ 
+-from __future__ import absolute_import, division, print_function, unicode_literals
++
+ 
+ import sys
+ import os
+@@ -77,7 +77,7 @@
+ 
+     all_tests_pass = True
+ 
+-    selected_chromosome = unicode(args.chr)
++    selected_chromosome = str(args.chr)
+     if args.debug: logger.info('Selected chromosome [%s]' % (selected_chromosome))
+ 
+     archive_paths = list()
+@@ -132,11 +132,11 @@
+                     all_chromosomes[chromosome] = 0
+                 all_chromosomes[chromosome] += 1
+ 
+-        common_chromosomes = [k for k, v in all_chromosomes.iteritems() if v == num_files]
++        common_chromosomes = [k for k, v in all_chromosomes.items() if v == num_files]
+         common_chromosomes.sort()
+         if args.debug: logger.info('Common chromosomes [%s]' % (','.join(common_chromosomes)))
+ 
+-        uncommon_chromosomes = [k for k, v in all_chromosomes.iteritems() if v != num_files]
++        uncommon_chromosomes = [k for k, v in all_chromosomes.items() if v != num_files]
+         uncommon_chromosomes.sort()
+         if args.debug: logger.info('Uncommon chromosomes [%s]' % (','.join(uncommon_chromosomes)))        
+ 
+Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py
+===================================================================
+--- bedops.orig/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py	2019-09-13 15:06:08.879696791 +0100
++++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasDuplicateElements.py	2019-09-13 15:06:08.871696823 +0100
+@@ -10,35 +10,35 @@
+ chr1_proc_out, chr1_proc_err = chr1_proc.communicate()
+ chr1_proc_out.strip('\n')
+ if int(chr1_proc_out) == 0:
+-    print "[STARCH] ERROR: chr1 is reporting it doesn't have a duplicate element, but it does!"
++    print("[STARCH] ERROR: chr1 is reporting it doesn't have a duplicate element, but it does!")
+     sys.exit(os.EX_USAGE)
+ 
+ chr2_proc = subprocess.Popen([unstarch, 'chr2', flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chr2_proc_out, chr2_proc_err = chr2_proc.communicate()
+ chr2_proc_out.strip('\n')
+ if int(chr2_proc_out) == 1:
+-    print "[STARCH] ERROR: chr2 is reporting it has a duplicate element, but it doesn't!"
++    print("[STARCH] ERROR: chr2 is reporting it has a duplicate element, but it doesn't!")
+     sys.exit(os.EX_USAGE)
+ 
+ chr3_proc = subprocess.Popen([unstarch, 'chr3', flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chr3_proc_out, chr3_proc_err = chr3_proc.communicate()
+ chr3_proc_out.strip('\n')
+ if int(chr3_proc_out) == 1:
+-    print "[STARCH] ERROR: chr3 is reporting it has a duplicate element, but it doesn't!"
++    print("[STARCH] ERROR: chr3 is reporting it has a duplicate element, but it doesn't!")
+     sys.exit(os.EX_USAGE)
+ 
+ chrAll_proc = subprocess.Popen([unstarch, 'all', flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chrAll_proc_out, chrAll_proc_err = chrAll_proc.communicate()
+ chrAll_proc_out.strip('\n')
+ if int(chrAll_proc_out) == 0:
+-    print "[STARCH] ERROR: 'all' chromosome usage is reporting the archive doesn't have a duplicate element, but there is a duplicate element in chr1!"
++    print("[STARCH] ERROR: 'all' chromosome usage is reporting the archive doesn't have a duplicate element, but there is a duplicate element in chr1!")
+     sys.exit(os.EX_USAGE)
+ 
+ chrOmit_proc = subprocess.Popen([unstarch, flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chrOmit_proc_out, chrOmit_proc_err = chrOmit_proc.communicate()
+ chrOmit_proc_out.strip('\n')
+ if int(chrOmit_proc_out) == 0:
+-    print "[STARCH] ERROR: omitted chromosome usage is reporting the archive doesn't have a duplicate element, but there is a duplicate element in chr1!"
++    print("[STARCH] ERROR: omitted chromosome usage is reporting the archive doesn't have a duplicate element, but there is a duplicate element in chr1!")
+     sys.exit(os.EX_USAGE)
+ 
+ sys.exit(os.EX_OK)
+Index: bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py
+===================================================================
+--- bedops.orig/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py	2019-09-13 15:06:08.879696791 +0100
++++ bedops/applications/bed/starch/test/nested_and_duplicate_elements/src/hasNestedElements.py	2019-09-13 15:06:08.871696823 +0100
+@@ -10,35 +10,35 @@
+ chr1_proc_out, chr1_proc_err = chr1_proc.communicate()
+ chr1_proc_out.strip('\n')
+ if int(chr1_proc_out) == 1:
+-    print "[STARCH] ERROR: chr1 is reporting it has a nested element, but it doesn't have one!"
++    print("[STARCH] ERROR: chr1 is reporting it has a nested element, but it doesn't have one!")
+     sys.exit(os.EX_USAGE)
+ 
+ chr2_proc = subprocess.Popen([unstarch, 'chr2', flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chr2_proc_out, chr2_proc_err = chr2_proc.communicate()
+ chr2_proc_out.strip('\n')
+ if int(chr2_proc_out) == 0:
+-    print "[STARCH] ERROR: chr2 is reporting it doesn't have a nested element, but it does!"
++    print("[STARCH] ERROR: chr2 is reporting it doesn't have a nested element, but it does!")
+     sys.exit(os.EX_USAGE)
+ 
+ chr3_proc = subprocess.Popen([unstarch, 'chr3', flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chr3_proc_out, chr3_proc_err = chr3_proc.communicate()
+ chr3_proc_out.strip('\n')
+ if int(chr3_proc_out) == 0:
+-    print "[STARCH] ERROR: chr3 is reporting it doesn't have a nested element, but it does!"
++    print("[STARCH] ERROR: chr3 is reporting it doesn't have a nested element, but it does!")
+     sys.exit(os.EX_USAGE)
+ 
+ chrAll_proc = subprocess.Popen([unstarch, 'all', flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chrAll_proc_out, chrAll_proc_err = chrAll_proc.communicate()
+ chrAll_proc_out.strip('\n')
+ if int(chrAll_proc_out) == 0:
+-    print "[STARCH] ERROR: 'all' chromosome usage is reporting the archive doesn't have a nested element, but there are nested elements in chr2 and chr3!"
++    print("[STARCH] ERROR: 'all' chromosome usage is reporting the archive doesn't have a nested element, but there are nested elements in chr2 and chr3!")
+     sys.exit(os.EX_USAGE)
+ 
+ chrOmit_proc = subprocess.Popen([unstarch, flag, archive], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ chrOmit_proc_out, chrOmit_proc_err = chrOmit_proc.communicate()
+ chrOmit_proc_out.strip('\n')
+ if int(chrOmit_proc_out) == 0:
+-    print "[STARCH] ERROR: omitted chromosome usage is reporting the archive doesn't have a nested element, but there are nested elements in chr2 and chr3!"
++    print("[STARCH] ERROR: omitted chromosome usage is reporting the archive doesn't have a nested element, but there are nested elements in chr2 and chr3!")
+     sys.exit(os.EX_USAGE)
+ 
+ sys.exit(os.EX_OK)
+Index: bedops/docs/conf.py
+===================================================================
+--- bedops.orig/docs/conf.py	2019-09-13 15:06:08.879696791 +0100
++++ bedops/docs/conf.py	2019-09-13 15:06:08.875696807 +0100
+@@ -42,8 +42,8 @@
+ master_doc = 'index'
+ 
+ # General information about the project.
+-project = u'BEDOPS'
+-copyright = u'2011-2019, Shane Neph, Alex Reynolds'
++project = 'BEDOPS'
++copyright = '2011-2019, Shane Neph, Alex Reynolds'
+ 
+ # The version info for the project you're documenting, acts as replacement for
+ # |version| and |release|, also used in various other places throughout the
+@@ -200,8 +200,8 @@
+ # Grouping the document tree into LaTeX files. List of tuples
+ # (source start file, target name, title, author, documentclass [howto/manual]).
+ latex_documents = [
+-  ('index', 'BEDOPS.tex', u'BEDOPS Documentation',
+-   u'Shane Neph, Alex Reynolds', 'manual'),
++  ('index', 'BEDOPS.tex', 'BEDOPS Documentation',
++   'Shane Neph, Alex Reynolds', 'manual'),
+ ]
+ 
+ # The name of an image file (relative to this directory) to place at the top of
+@@ -230,8 +230,8 @@
+ # One entry per manual page. List of tuples
+ # (source start file, name, description, authors, manual section).
+ man_pages = [
+-    ('index', 'bedops', u'BEDOPS Documentation',
+-     [u'Shane Neph, Alex Reynolds'], 1)
++    ('index', 'bedops', 'BEDOPS Documentation',
++     ['Shane Neph, Alex Reynolds'], 1)
+ ]
+ 
+ # If true, show URL addresses after external links.
+@@ -244,8 +244,8 @@
+ # (source start file, target name, title, author,
+ #  dir menu entry, description, category)
+ texinfo_documents = [
+-  ('index', 'BEDOPS', u'BEDOPS Documentation',
+-   u'Shane Neph, Alex Reynolds', 'BEDOPS', 'One line description of project.',
++  ('index', 'BEDOPS', 'BEDOPS Documentation',
++   'Shane Neph, Alex Reynolds', 'BEDOPS', 'One line description of project.',
+    'Miscellaneous'),
+ ]
+ 
+@@ -265,10 +265,10 @@
+ # -- Options for Epub output ---------------------------------------------------
+ 
+ # Bibliographic Dublin Core info.
+-epub_title = u'BEDOPS'
+-epub_author = u'Shane Neph, Alex Reynolds'
+-epub_publisher = u'Shane Neph, Alex Reynolds'
+-epub_copyright = u'2013, Shane Neph, Alex Reynolds'
++epub_title = 'BEDOPS'
++epub_author = 'Shane Neph, Alex Reynolds'
++epub_publisher = 'Shane Neph, Alex Reynolds'
++epub_copyright = '2013, Shane Neph, Alex Reynolds'
+ 
+ # The language of the text. It defaults to the language option
+ # or en if the language is not set.

debian/patches/series

+2to3.patch
 use_debian_libs
 hardening.patch